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On 19/01/2012 11:27 PM, Chandan Choudhury wrote:
<blockquote
cite="mid:CAHESojx-Jx=5vMR5SWgZh+Qb4d6381qzJtN-5V2rUUjoNA97pw@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk
Wassenaar <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Chandan,<br>
<br>
The box is accessible from the t_trxframe struct. Assuming you
have<br>
<br>
t_trxframe *fr<br>
<br>
You can access it through<br>
<br>
fr->box<br>
</blockquote>
<div><br>
</div>
<div>Thanks Tsjerk. It (fr.box) did help me to get the box
coordinates.</div>
<div><br>
</div>
<div>fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me
the values but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which
seems to me that the origin of the box is at (0,0,0). </div>
</div>
</blockquote>
<br>
The origin is always at (0,0,0) by definition, not by the contents
of fr.box. There's no magic center of a periodic box, either.<br>
<br>
fr.box has the box dimensions, which in general require more than
the 3 pieces of information required for a rectangular solid box.<br>
<br>
<blockquote
cite="mid:CAHESojx-Jx=5vMR5SWgZh+Qb4d6381qzJtN-5V2rUUjoNA97pw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>Then, fr.box[XX][XX] is the maximum
X-coordinate, fr.box[YY][YY] is the maximum
Y-coordinate,fr.box[ZZ][ZZ] is the maximum Z-coordinate. Am I
correct?</div>
</div>
</blockquote>
<br>
For some box types, yes.<br>
<br>
Mark<br>
<br>
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cite="mid:CAHESojx-Jx=5vMR5SWgZh+Qb4d6381qzJtN-5V2rUUjoNA97pw@mail.gmail.com"
type="cite">
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<div><br>
</div>
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<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
But if you remove jumps first, you're fine anyway. Just don't
put<br>
things back in the box afterwards. And don't center if your
aim is<br>
calculating MSDs.<br>
</blockquote>
<div><br>
</div>
<div>Yeah, you are right.</div>
<div><br>
</div>
<div>Chandan</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<div class="HOEnZb">
<div class="h5"><br>
On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury <<a
moz-do-not-send="true" href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a>>
wrote:<br>
><br>
><br>
> On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham <<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> wrote:<br>
>><br>
>> On 19/01/2012 5:39 PM, Chandan Choudhury wrote:<br>
>>><br>
>>><br>
>>> Dear gmx-users,<br>
>>><br>
>>> I have a simulated a system containing a
linear polymer in a cubic box<br>
>>> with water molecules. I need to get rid of
PBC effect on the system such<br>
>>> that I can execute my own analysis code. I
intend to compute the msd of<br>
>>> water molecules along the polymer backbone.<br>
>><br>
>><br>
>> You can't "get rid of PBC", you can only manage
it. The question reduces<br>
>> what you want to see if a molecule diffuses
across the periodic boundary<br>
>> from near one end of the polymer to the other
end.<br>
>><br>
>><br>
>>> So, when I execute my own analysis code, I
see the msd's are abrupt (i.e<br>
>>> very high), this is due to the pbc. So, for
getting rid of PBC effect, I<br>
>>> performed the suggested trjconv workflow<br>
>>> (<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a>).<br>
>>><br>
>>> Below are my executed commands :<br>
>>><br>
>>> # Made the system whole<br>
>>><br>
>>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f
0-4.xtc -pbc whole -o<br>
>>> 0-4_whole.xtc<br>
>>><br>
>>> # 0 is the whole system. md0-4.tpr is the
initial tpr file containing<br>
>>> whole (no broken) polymer inside the cubic
box.<br>
>>> # Extracted 1st frame from the initial
trajectory<br>
>>><br>
>>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f
0-4.xtc -pbc nojump -o 1st.pdb<br>
>>> -dump 0<br>
>>><br>
>>> # used the whole trajectory to remove jumps
with reference to the 1st<br>
>>> frame.<br>
>>> echo 0 | trjconv_4.5.5 -s 1st.pdb -f
0-4_whole.xtc -pbc nojump -o<br>
>>> 0-4_nojump.xtc<br>
>><br>
>><br>
>> So here you said "let molecules diffuse away from
the solute".<br>
>><br>
>><br>
>>><br>
>>> #system is being centered<br>
>>> echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f
0-4_nojump.xtc -o<br>
>>> 0-4_center.xtc -center<br>
>>><br>
>>> #putting every atom in the box<br>
>>> echo 0 | trjconv -s md0-4.tpr -f
0-4_center.xtc -o 0-4_box.xtc -pbc atom<br>
>><br>
>><br>
>> ... and now you said "take all the atoms and put
them back in the box",<br>
>> creating jumps whenever one crosses the
boundaries.<br>
>><br>
>><br>
>>><br>
>>> Still when I execute my analysis code, I do
see the abrupt behaviour in<br>
>>> the msd plot. Can someone guide me how to
completely get rid of PBC<br>
>>> artifacts.<br>
>><br>
>><br>
>> Don't simulate with them :-P Is your analysis
technique sound for the<br>
>> periodic case?<br>
><br>
><br>
> No, my analysis code doesnot take care of PBC. As to
deal with PBC, I need<br>
> to have the box vectors (for atleast NPT simulation)
from the trajectory and<br>
> I am unable to extract the box vectors (as of date).<br>
><br>
> Chandan<br>
><br>
>><br>
>><br>
>> Mark<br>
>><br>
>> --<br>
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><br>
><br>
><br>
> --<br>
> Chandan kumar Choudhury<br>
> NCL, Pune<br>
> INDIA<br>
><br>
><br>
> --<br>
> gmx-users mailing list <a moz-do-not-send="true"
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<br>
<br>
--<br>
</div>
</div>
<div class="im HOEnZb">Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and
Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
</div>
<div class="HOEnZb">
<div class="h5">--<br>
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